External Email - Use Caution
DearFreesurfer developers,
when trying to run trac-all -prep I am running into this error
gbw-d-m0128:DIFFUSION r0755008$ trac-all -prep -c
/Users/r0755008/Desktop/mri_data/TRACULA/TRACULA_CONFIGURATION_FILE.txt
domainname: Command not found.
Too many ('s.
ERROR: Syntax error in configuration file
/Users/r0755008/Desktop/mri_data/TRACULA/TRACULA_CONFIGURATION_FILE.txt
I checked the file but there seem to be no errors in the ('s.
This error has previously been encountered
https://secure-web.cisco.com/1sKX4EXSdl-lzzKBfb369ful1KJMpWkExgYjXUfdMyAgEiLxmN-7MUWuEnZfe6fFIgowB68U2mNgao0KjS4PAfFLRsTmh7OkFg6D4IV4CMi-68OueIKNIDatn-hDv1YZ15W7tXz_fi2msIxxR_qP6YQk4asNuiMw9V9LHaembEzvAAr-oMUyw8yw_mrwjKGcR189BLip2OKFKDJS1qiS9UVHptmlDleX7ja_VsDq6QHHrrE2n0R8vFbYXAM1IkF6tbv6cfSKV91f3sbBxrvJgl16Yba47czO4agSUB9yuP0UTkvcJfaHXzQ6nM7-r0Xvq/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg70662.html%23
but there is no solution proposed for the facts that the domainname command is
missing from my mac in the /usr/bin folder. What can i do to solve this error.
In the attachments you can find the tracula config file if this would be
helpful. Thank you for the help.
Kind regards,
Ward Deferm
# T1 images and FreeSurfer segmentations are expected to be found here
setenv SUBJECTS_DIR /Users/r0755008/Desktop/mri_data/STRUCT
# Output directory where trac-all results will be saved
# Default: Same as SUBJECTS_DIR
#
set dtroot = /Users/r0755008/Desktop/mri_data/TRACULA
# Subject IDs
# Here each subject is listed twice because it has two diffusion scans
#
set subjlist = (NT001 \
NT001 \
NT002 \
NT002 \
NT003 \
NT003 \
NT004 \
NT004 \
NT005 \
NT005 \
NT006 \
NT006 \
NT007 \
NT007 \
NT009 \
NT009 \
NT010 \
NT010 \
NT011 \
NT011 \
NT012 \
NT012 \
NT013 \
NT013 \
NT014 \
NT014 \
NT015 \
NT015 \
NT016 \
NT016 \
NT017 \
NT017 \
NT018 \
NT018 \
NT020 \
NT020 \
NT021 \
NT021 \
NT024 \
NT024 \
NT025 \
NT025 \
NT026 \
NT026 \
NT027 \
NT027 \
NT028 \
NT028 \
NT029 \
NT029 \
NT030 \
NT030 \
NT032 \
NT032 \
NT033 \
NT033 \
NT034 \
NT034 \
NT035 \
NT035 \
NT036 \
NT036 \
NT037 \
NT037 \
NT038 \
NT038 \
NT039 \
NT039 \
NT040 \
NT040 \
PT002 \
PT002 \
PT003 \
PT003 \
PT004 \
PT004 \
PT005 \
PT005 \
PT007 \
PT007 \
PT008 \
PT008 \
PT010 \
PT010 \
PT011 \
PT011 \
PT013 \
PT013 \
PT014 \
PT014 \
PT015 \
PT015 \
PT016 \
PT017 \
PT018 \
PT018 \
PT019 \
PT019 \
PT020 \
PT020 \
PT021 \
PT021 \
PT022 \
PT022 \
PT023 \
PT023 \
PT024 \
PT024 \
PT025 \
PT025 \
PT026 \
PT026 \
PT027 \
PT027 \
PT028 \
PT028 \
PT029 \
PT029 \
PT030 \
PT030 \
PT030 \
PT031 \
PT031 \
PT032 \
PT032 \
PT033 \
PT033 \
PT034 \
PT034 \
PT035 \
PT035 \
PT036 \
PT036 \
PT037 \
PT037 \
PT038 \
PT038 \
PT039 \
PT039 \
PT040 \
PT040)
# Input diffusion DICOMs (file names relative to dcmroot)
# If original DICOMs don't exist, these can be in other image format
# but then the gradient table and b-value table must be specified (see below)
#note change to own files
set dcmroot = /Users/r0755008/Desktop/mri_data/DIFFUSION
set dcmlist = (NT001/front.nii \
NT001/reverse.nii \
NT002/front.nii \
NT002/reverse.nii \
NT003/front.nii \
NT003/reverse.nii \
NT004/front.nii \
NT004/reverse.nii \
NT005/front.nii \
NT005/reverse.nii \
NT006/front.nii \
NT006/reverse.nii \
NT007/front.nii \
NT007/reverse.nii \
NT009/front.nii \
NT009/reverse.nii \
NT010/front.nii \
NT010/reverse.nii \
NT011/front.nii \
NT011/reverse.nii \
NT012/front.nii \
NT012/reverse.nii \
NT013/front.nii \
NT013/reverse.nii \
NT014/front.nii \
NT014/reverse.nii \
NT015/front.nii \
NT015/reverse.nii \
NT016/front.nii \
NT016/reverse.nii \
NT017/front.nii \
NT017/reverse.nii \
NT018/front.nii \
NT018/reverse.nii \
NT020/front.nii \
NT020/reverse.nii \
NT021/front.nii \
NT021/reverse.nii \
NT024/front.nii \
NT024/reverse.nii \
NT025/front.nii \
NT025/reverse.nii \
NT026/front.nii \
NT026/reverse.nii \
NT027/front.nii \
NT027/reverse.nii \
NT028/front.nii \
NT028/reverse.nii \
NT029/front.nii \
NT029/reverse.nii \
NT030/front.nii \
NT030/reverse.nii \
NT032/front.nii \
NT032/reverse.nii \
NT033/front.nii \
NT033/reverse.nii \
NT034/front.nii \
NT034/reverse.nii \
NT035/front.nii \
NT035/reverse.nii \
NT036/front.nii \
NT036/reverse.nii \
NT037/front.nii \
NT037/reverse.nii \
NT038/front.nii \
NT038/reverse.nii \
NT039/front.nii \
NT039/reverse.nii \
NT040/front.nii \
NT040/reverse.nii \
PT002/front.nii \
PT002/reverse.nii \
PT003/front.nii \
PT003/reverse.nii \
PT004/front.nii \
PT004/reverse.nii \
PT005/front.nii \
PT005/reverse.nii \
PT007/front.nii \
PT007/reverse.nii \
PT008/front.nii \
PT008/reverse.nii \
PT010/front.nii \
PT010/reverse.nii \
PT011/front.nii \
PT011/reverse.nii \
PT013/front.nii \
PT013/reverse.nii \
PT014/front.nii \
PT014/reverse.nii \
PT015/front.nii \
PT015/reverse.nii \
PT016/front.nii \
PT016/reverse.nii \
PT017/front.nii \
PT017/reverse.nii \
PT018/front.nii \
PT018/reverse.nii \
PT019/front.nii \
PT019/reverse.nii \
PT020/front.nii \
PT020/reverse.nii \
PT021/front.nii \
PT021/reverse.nii \
PT022/front.nii \
PT022/reverse.nii \
PT023/front.nii \
PT023/reverse.nii \
PT024/front.nii \
PT024/reverse.nii \
PT025/front.nii \
PT025/reverse.nii \
PT026/front.nii \
PT027/reverse.nii \
PT028/front.nii \
PT028/reverse.nii \
PT029/front.nii \
PT029/reverse.nii \
PT030/front.nii \
PT030/reverse.nii \
PT031/front.nii \
PT031/reverse.nii \
PT032/front.nii \
PT032/reverse.nii \
PT033/front.nii \
PT033/reverse.nii \
PT034/front.nii \
PT034/reverse.nii \
PT035/front.nii \
PT035/reverse.nii \
PT036/front.nii \
PT036/reverse.nii \
PT037/front.nii \
PT037/reverse.nii \
PT038/front.nii \
PT038/reverse.nii \
PT039/front.nii \
PT039/reverse.nii \
PT040/front.nii \
PT040/reverse.nii)
# Diffusion gradient tables (file names can be relative to dcmroot)
# Must be specified only if they cannot be read from the DICOM headers
# The tables must have either three columns, where each row is a gradient vector
# or three rows, where each column is a gradient vector
# There must be as many gradient vectors as volumes in the diffusion data set
# Default: Read from DICOM header
#
set bveclist = (NT001/front.bvec \
NT001/reverse.bvec \
NT002/front.bvec \
NT002/reverse.bvec \
NT003/front.bvec \
NT003/reverse.bvec \
NT004/front.bvec \
NT004/reverse.bvec \
NT005/front.bvec \
NT005/reverse.bvec \
NT006/front.bvec \
NT006/reverse.bvec \
NT007/front.bvec \
NT007/reverse.bvec \
NT009/front.bvec \
NT009/reverse.bvec \
NT010/front.bvec \
NT010/reverse.bvec \
NT011/front.bvec \
NT011/reverse.bvec \
NT012/front.bvec \
NT012/reverse.bvec \
NT013/front.bvec \
NT013/reverse.bvec \
NT014/front.bvec \
NT014/reverse.bvec \
NT015/front.bvec \
NT015/reverse.bvec \
NT016/front.bvec \
NT016/reverse.bvec \
NT017/front.bvec \
NT017/reverse.bvec \
NT018/front.bvec \
NT018/reverse.bvec \
NT020/front.bvec \
NT020/reverse.bvec \
NT021/front.bvec \
NT021/reverse.bvec \
NT024/front.bvec \
NT024/reverse.bvec \
NT025/front.bvec \
NT025/reverse.bvec \
NT026/front.bvec \
NT026/reverse.bvec \
NT027/front.bvec \
NT027/reverse.bvec \
NT028/front.bvec \
NT028/reverse.bvec \
NT029/front.bvec \
NT029/reverse.bvec \
NT030/front.bvec \
NT030/reverse.bvec \
NT032/front.bvec \
NT032/reverse.bvec \
NT033/front.bvec \
NT033/reverse.bvec \
NT034/front.bvec \
NT034/reverse.bvec \
NT035/front.bvec \
NT035/reverse.bvec \
NT036/front.bvec \
NT036/reverse.bvec \
NT037/front.bvec \
NT037/reverse.bvec \
NT038/front.bvec \
NT038/reverse.bvec \
NT039/front.bvec \
NT039/reverse.bvec \
NT040/front.bvec \
NT040/reverse.bvec \
PT002/front.bvec \
PT002/reverse.bvec \
PT003/front.bvec \
FT003/reverse.bvec \
PT004/front.bvec \
PT004/reverse.bvec \
PT005/front.bvec \
PT005/reverse.bvec \
PT007/front.bvec \
PT007/reverse.bvec \
PT008/front.bvec \
PT008/reverse.bvec \
PT010/front.bvec \
PT010/reverse.bvec \
PT011/front.bvec \
PT011/reverse.bvec \
PT013/front.bvec \
PT013/reverse.bvec \
PT014/front.bvec \
PT014/reverse.bvec \
PT015/front.bvec \
PT015/reverse.bvec \
PT016/front.bvec \
PT016/reverse.bvec \
PT017/front.bvec \
PT018/reverse.bvec \
PT019/front.bvec \
PT019/reverse.bvec \
PT020/front.bvec \
PT020/reverse.bvec \
PT021/front.bvec \
PT021/reverse.bvec \
PT022/front.bvec \
PT022/reverse.bvec \
PT023/front.bvec \
PT023/reverse.bvec \
PT024/front.bvec \
PT024/reverse.bvec \
PT025/front.bvec \
PT025/reverse.bvec \
PT026/front.bvec \
PT026/reverse.bvec \
PT027/front.bvec \
PT027/reverse.bvec \
PT028/front.bvec \
PT028/reverse.bvec \
PT029/front.bvec \
PT029/reverse.bvec \
PT030/front.bvec \
PT030/reverse.bvec \
PT031/front.bvec \
PT031/reverse.bvec \
PT032/front.bvec \
PT032/reverse.bvec \
PT033/front.bvec \
PT033/reverse.bvec \
PT034/front.bvec \
PT034/reverse.bvec \
PT035/front.bvec \
PT035/reverse.bvec \
PT036/front.bvec \
PT036/reverse.bvec \
PT037/front.bvec \
PT037/reverse.bvec \
PT038/front.bvec \
PT038/reverse.bvec \
PT039/front.bvec \
PT039/reverse.bvec \
PT040/front.bvec \
PT040/reverse.bvec)
# Diffusion b-value tables (file names can be relative to dcmroot)
# Must be specified only if they cannot be read from the DICOM headers
# There must be as many b-values as volumes in the diffusion data set
# Default: Read from DICOM header
#
set bvallist = (NT001/front.bval \
NT001/reverse.bval \
NT002/front.bval \
NT002/reverse.bval \
NT003/front.bval \
NT003/reverse.bval \
NT004/front.bval \
NT004/reverse.bval \
NT005/front.bval \
NT005/reverse.bval \
NT006/front.bval \
NT006/reverse.bval \
NT007/front.bval \
NT007/reverse.bval \
NT009/front.bval \
NT009/reverse.bval \
NT010/front.bval \
NT010/reverse.bval \
NT011/front.bval \
NT011/reverse.bval \
NT012/front.bval \
NT012/reverse.bval \
NT013/front.bval \
NT013/reverse.bval \
NT014/front.bval \
NT014/reverse.bval \
NT015/front.bval \
NT015/reverse.bval \
NT016/front.bval \
NT016/reverse.bval \
NT017/front.bval \
NT017/reverse.bval \
NT018/front.bval \
NT018/reverse.bval \
NT020/front.bval \
NT020/reverse.bval \
NT021/front.bval \
NT021/reverse.bval \
NT024/front.bval \
NT024/reverse.bval \
NT025/front.bval \
NT025/reverse.bval \
NT026/front.bval \
NT026/reverse.bval \
NT027/front.bval \
NT027/reverse.bval \
NT028/front.bval \
NT028/reverse.bval \
NT029/front.bval \
NT029/reverse.bval \
NT030/front.bval \
NT030/reverse.bval \
NT032/front.bval \
NT032/reverse.bval \
NT033/front.bval \
NT033/reverse.bval \
NT034/front.bval \
NT034/reverse.bval \
NT035/front.bval \
NT035/reverse.bval \
NT036/front.bval \
NT036/reverse.bval \
NT037/front.bval \
NT037/reverse.bval \
NT038/front.bval \
NT038/reverse.bval \
NT039/front.bval \
NT039/reverse.bval \
NT040/front.bval \
NT040/reverse.bval \
PT002/front.bval \
PT002/reverse.bval \
PT003/front.bval \
PT003/reverse.bval \
PT004/front.bval \
PT004/reverse.bval \
PT005/front.bval \
PT005/reverse.bval \
PT007/front.bval \
PT007/reverse.bval \
PT008/front.bval \
PT008/reverse.bval \
PT010/front.bval \
PT010/reverse.bval \
PT011/front.bval \
PT011/reverse.bval \
PT013/front.bval \
PT013/reverse.bval \
PT014/front.bval \
PT014/reverse.bval \
PT015/front.bval \
PT015/reverse.bval \
PT016/front.bval \
PT016/reverse.bval \
PT017/front.bval \
PT017/reverse.bval \
PT018/front.bval \
PT018/reverse.bval \
PT019/front.bval \
PT019/reverse.bval \
PT020/front.bval \
PT020/reverse.bval \
PT021/front.bval \
PT021/reverse.bval \
PT022/front.bval \
PT023/reverse.bval \
PT024/front.bval \
PT024/reverse.bval \
PT025/front.bval \
PT025/reverse.bval \
PT026/front.bval \
PT026/reverse.bval \
PT027/front.bval \
PT027/reverse.bval \
PT028/front.bval \
PT028/reverse.bval \
PT029/front.bval \
PT029/reverse.bval \
PT030/front.bval \
PT030/reverse.bval \
PT031/front.bval \
PT031/reverse.bval \
PT032/front.bval \
PT032/reverse.bval \
PT033/front.bval \
PT033/reverse.bval \
PT034/front.bval \
PT034/reverse.bval \
PT035/front.bval \
PT035/reverse.bval \
PT036/front.bval \
PT036/reverse.bval \
PT037/front.bval \
PT037/reverse.bval \
PT038/front.bval \
PT038/reverse.bval \
PT039/front.bval \
PT039/reverse.bval \
PT040/front.bval \
PT040/reverse.bval)
# Perform correction for B0 inhomogeneity distortions?
# 0: No correction (default)
# 1: Perform correction based on a field map
# Requires additional inputs (see below): b0mlist, b0plist, echospacing
# 2: Perform correction based on reverse-polarity images
# Requires additional inputs (see below): echospacing, pedir, epifactor
#
set dob0 = 2
# Echo spacing (this is found in the scanner protocol printout)
# Only used if dob0 = 1 or 2
# Default: None
#
set echospacing = 0.227045
# Phase-encode direction (this is found in the scanner protocol printout)
# One for each diffusion scan above (must differ between runs in a session)
# In this example, each session contains an AP- and a PA-encoded diffusion scan
# Only used if dob0 = 2
# Default: None
#
set pedir = (AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA
AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA
AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA
AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA
AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA
AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA
AP PA AP PA AP PA AP PA AP PA AP PA)
# EPI factor (this is found in the scanner protocol printout)
# Only used if dob0 = 2
# Default: None
#
set epifactor = 57
# Perform correction for eddy-current distortions?
# 0: No correction
# 1: Perform registration-based correction with eddy_correct
# 2: Perform model-based correction with eddy (default)
#
set doeddy = 2
# Rotate diffusion gradient vectors to match eddy-current compensation?
# Only used if doeddy = 1 or 2
# Default: 1 (yes)
#
set dorotbvecs = 1
# Intra-subject (diffusion-to-T1) registration method
# 1: Affine with a correlation ratio cost
# 2: Affine with a mutual information cost
# 3: Affine with a boundary-based cost (default)
#
set intrareg = 3
# Degrees of freedom for intra-subject registration
# Can be 6 (rigid), 9 (rigid+scaling), or 12 (full affine)
# Default: 6 for infants, 9 otherwise
#
set intradof = 9
# Maximum rotation angle (degrees) for intra-subject registration
# Default: 3 for infants, 90 otherwise
#
set intrarot = 90
# Inter-subject registration method
# 1: Affine T1-to-T1 with a correlation ratio cost
# 2: Affine T1-to-T1 with a mutual information cost
# 3: Affine T1-to-T1 with a robust cost (default for infants)
# 4: Nonlinear T1-to-T1 with CVS
# 5: Nonlinear FA-to-FA with SyN (default)
#
set interreg = 5
# Whole-brain segmentation used to extract the anatomical neighborhood priors
# of the pathways of interest
# Must exist in each subject's FreeSurfer recon directory, under:
# $SUBJECTS_DIR/$subjid/mri/$segname.mgz
# Default: aparc+aseg
#
set segname = aparc+aseg
# Use the thalamic nuclei segmentation?
# This is highly recommended to use for any pathways that terminate in
# or neighbor the thalamus
# When used, it is merged with the whole-brain segmentation above
# Must exist in each subject's FreeSurfer recon directory, under:
# $SUBJECTS_DIR/$subjid/mri/ThalamicNuclei.v12.T1.FSvoxelSpace.mgz
# Default: 1 (yes)
#
set usethalnuc = 1
# Use brain mask extracted from T1 image instead of low-b diffusion image?
# Has no effect if there is no T1 data
# Default: 1 (yes)
#
set usemaskanat = 1
# Fractional intensity threshold for BET mask extraction from low-b images
# This mask is used only if usemaskanat = 0
# Default: 0.3
#
set thrbet = 0.3
# Paths to reconstruct
# Default: All paths in $FREESURFER_HOME/trctrain/hcp/pathlist.txt
#
set pathlist = (lh.uf rh.uf lh.ilf rh.ilf lh.slf1 rh.slf1 lh.slf2 rh.slf2
lh.slf3 rh.slf3)
# Number of path control points
# It can be a single number for all paths or a different number for each of the
# paths specified in pathlist (recommended, with more points for longer paths)
# Default: As in $FREESURFER_HOME/trctrain/hcp/pathlist.txt
#
#set ncpts = ( 7 7 5 )
# Number of "sticks" (anisotropic diffusion compartments) in the bedpostx
# ball-and-stick model
# Default: 2
#
set nstick = 2
# Number of MCMC burn-in iterations
# (Path samples drawn initially by MCMC algorithm and discarded)
# Default: 200
#
set nburnin = 500
# Number of MCMC iterations
# (Path samples drawn by MCMC algorithm and used to estimate path distribution)
# Default: 7500
#
set nsample = 7500
# Frequency with which MCMC path samples are retained for path distribution
# Default: 5 (keep every 5th sample)
#
set nkeep = 5
# Reinitialize path reconstruction?
# This is an option of last resort, to be used only if one of the reconstructed
# pathway distributions looks like a single curve. This is a sign that the
# initial guess for the pathway was problematic, perhaps due to poor alignment
# between the individual and the atlas. Setting the reinit parameter to 1 and
# rerunning "trac-all -prior" and "trac-all -path", only for the specific
# subjects and pathways that had this problem, will attempt to reconstruct them
# with a different initial guess.
# Default: 0 (do not reinitialize)
#
set reinit = 0
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